VMD-L Mailing List

From: Andreas Kukol (a.kukol_at_herts.ac.uk)
Date: Fri Apr 26 2019 - 04:30:30 CDT

Dear João,

The link to the new version of VMD seemed to be the alpha version, so as a beginner I better stick with VMD 1.9.3

I could not create the \usr\tmp folder as I don't have write permission for that. I tried to define the variable VMDTMPDIR in .vmdrc:

set env(VMDTMPDIR) /home/akukol/vmdtmp

and verified in the vmd console that the variable was set. It still did not work.

Then I tried in .vmdrc: set VMDTMPDIR and finally in my .bashrc: export VMDTMPDIR=/home/akukol/vmdtmp

But the problem remained: Unable to open file /usr/tmp/torplot_temp.pdb for writing

Many thanks
Andreas

>-----Original Message-----
>From: Joao Ribeiro [mailto:jribeiro_at_ks.uiuc.edu]
>Sent: 25 April 2019 19:32
>To: Andreas Kukol; vmd-l_at_ks.uiuc.edu
>Subject: Re: vmd-l: QwikMD Glycoside Hydrolase Tutorial step 2
>
>Dear Andreas,
>
>Thank you for reporting the error. In fact, old versions of QwikMD (and VMD)
>had issues with Ubuntu due to the missing "/usrt/tmp/" folder. These and other
>issues were corrected in the new versions of VMD, which I would recommend
>to use.
>https://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName
>=VMD
>
>If some reason you don't want to update VMD, you can create the folder
>manually, or direct VMD to an existing folder to be used as a temporary folder
>by defining the variable env(VMDTMPDIR) in the .vmdrc file.
>
>Again, the new versions of VMD have more updates and fixes than just this one.
>
>There is also an updated version of QwikMD (QwikMD beta) that you can install.
>Please download QwikMD beta from
>http://www.ks.uiuc.edu/Research/qwikmd/.
>
>I hope this help
>
>Best
>
>João
>
>
>……………………………………………………...
>João Vieira Ribeiro
>Theoretical and Computational Biophysics Group Beckman Institute, University
>of Illinois http://www.ks.uiuc.edu/~jribeiro/ jribeiro_at_illinois.edu
>+1 (217) 3005851
>
>On 4/25/19, 10:35 AM, "Andreas Kukol" <owner-vmd-l_at_ks.uiuc.edu on behalf
>of a.kukol_at_herts.ac.uk> wrote:
>
> Hello,
>
> I am trying to work though the 1-page QwikMD Glycoside Hydrolase Tutorial
>and encountered the following problems:
>
> Step 2: Load Glycoside Hydrolase by typing 7CEL
> ERROR) BaseMolecule: init_atoms called with invalid number of atoms: 0
>
> Fixed this by downloading 7CEL.pdb manually and then browse and load the
>molecule into QwikMD
>
> Step 2:
> Unable to open file /usr/tmp/torplot_temp.pdb for writing
> ERROR) Unable to open file /usr/tmp/torplot_temp.pdb of type pdb for
>writing frames.
>
> I think this is caused by lacking write permission to the /usr folder, but I am
>not sure how to fix that.
>
> I am using VMD 1.9.3 installed in /home/akukol/vmd-1.9.3 (this is were all the
>files are) and /home/akukol/bin/ for the startup script. LINUX Kubuntu 18.04
>
> Many thanks
> Andreas
>
>
>
>
>